Multiple sequence alignment - TraesCS1D01G093500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G093500 chr1D 100.000 3776 0 0 1 3776 79142610 79138835 0.000000e+00 6974
1 TraesCS1D01G093500 chr1D 80.451 266 50 2 150 414 86205044 86205308 6.400000e-48 202
2 TraesCS1D01G093500 chr1B 96.739 3772 121 2 1 3770 130356561 130352790 0.000000e+00 6283
3 TraesCS1D01G093500 chr1B 88.382 2281 237 21 660 2925 130024222 130021955 0.000000e+00 2719
4 TraesCS1D01G093500 chr1B 91.234 867 65 4 2918 3774 130021454 130020589 0.000000e+00 1170
5 TraesCS1D01G093500 chr1A 94.830 2205 78 13 1 2196 97957273 97955096 0.000000e+00 3408
6 TraesCS1D01G093500 chr1A 94.588 1589 83 3 2188 3774 97954911 97953324 0.000000e+00 2455
7 TraesCS1D01G093500 chr1A 87.298 1669 201 10 2091 3751 97807002 97805337 0.000000e+00 1897
8 TraesCS1D01G093500 chr1A 87.500 1232 148 4 850 2076 97809181 97807951 0.000000e+00 1417
9 TraesCS1D01G093500 chr4D 74.491 2752 613 67 853 3547 3347614 3344895 0.000000e+00 1110
10 TraesCS1D01G093500 chr4D 74.860 2319 513 55 854 3127 1708236 1705943 0.000000e+00 989
11 TraesCS1D01G093500 chr6B 77.076 1409 292 27 1004 2394 158167040 158168435 0.000000e+00 784
12 TraesCS1D01G093500 chr6B 82.206 281 48 2 150 429 52180037 52179758 1.360000e-59 241
13 TraesCS1D01G093500 chr6D 75.605 1406 295 31 1004 2394 83163090 83164462 0.000000e+00 652
14 TraesCS1D01G093500 chr2B 75.318 1414 309 31 1004 2394 754921295 754922691 3.180000e-180 641
15 TraesCS1D01G093500 chr2B 73.959 1417 308 50 2035 3414 693336545 693337937 2.010000e-142 516
16 TraesCS1D01G093500 chr2B 78.648 281 54 6 149 426 693837949 693838226 8.330000e-42 182
17 TraesCS1D01G093500 chr2B 79.032 248 52 0 150 397 693321662 693321909 1.800000e-38 171
18 TraesCS1D01G093500 chr2B 75.073 341 77 6 149 487 693334159 693334493 6.530000e-33 152
19 TraesCS1D01G093500 chr2B 73.977 342 82 6 150 489 693448016 693448352 8.510000e-27 132
20 TraesCS1D01G093500 chr3D 76.568 1148 241 24 1003 2136 600154471 600155604 4.170000e-169 604
21 TraesCS1D01G093500 chr3D 75.547 274 61 6 144 414 613839628 613839898 3.060000e-26 130


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G093500 chr1D 79138835 79142610 3775 True 6974.0 6974 100.000 1 3776 1 chr1D.!!$R1 3775
1 TraesCS1D01G093500 chr1B 130352790 130356561 3771 True 6283.0 6283 96.739 1 3770 1 chr1B.!!$R1 3769
2 TraesCS1D01G093500 chr1B 130020589 130024222 3633 True 1944.5 2719 89.808 660 3774 2 chr1B.!!$R2 3114
3 TraesCS1D01G093500 chr1A 97953324 97957273 3949 True 2931.5 3408 94.709 1 3774 2 chr1A.!!$R2 3773
4 TraesCS1D01G093500 chr1A 97805337 97809181 3844 True 1657.0 1897 87.399 850 3751 2 chr1A.!!$R1 2901
5 TraesCS1D01G093500 chr4D 3344895 3347614 2719 True 1110.0 1110 74.491 853 3547 1 chr4D.!!$R2 2694
6 TraesCS1D01G093500 chr4D 1705943 1708236 2293 True 989.0 989 74.860 854 3127 1 chr4D.!!$R1 2273
7 TraesCS1D01G093500 chr6B 158167040 158168435 1395 False 784.0 784 77.076 1004 2394 1 chr6B.!!$F1 1390
8 TraesCS1D01G093500 chr6D 83163090 83164462 1372 False 652.0 652 75.605 1004 2394 1 chr6D.!!$F1 1390
9 TraesCS1D01G093500 chr2B 754921295 754922691 1396 False 641.0 641 75.318 1004 2394 1 chr2B.!!$F4 1390
10 TraesCS1D01G093500 chr2B 693334159 693337937 3778 False 334.0 516 74.516 149 3414 2 chr2B.!!$F5 3265
11 TraesCS1D01G093500 chr3D 600154471 600155604 1133 False 604.0 604 76.568 1003 2136 1 chr3D.!!$F1 1133

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
812 845 0.827507 ACGGCAAATCCTTTGTGGCT 60.828 50.000 1.97 0.0 42.56 4.75 F
2503 4218 2.195922 GCAGCTTTGGTTCAACAAGTG 58.804 47.619 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 4274 2.985809 CTCGCATATGCTAGAGTGAAGC 59.014 50.000 24.56 0.0 36.09 3.86 R
3680 5925 2.631062 TCCCAACTTAGTGAGCTTCGAA 59.369 45.455 0.00 0.0 0.00 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 49 9.390795 CACATTCGTAAGTAGTATGTACATACC 57.609 37.037 32.70 22.28 40.78 2.73
113 116 3.797039 CATCTCGAAATGGTTCCAGCTA 58.203 45.455 0.00 0.00 0.00 3.32
511 514 1.133976 ACTGCTCACAAACTCAGGCTT 60.134 47.619 0.00 0.00 0.00 4.35
515 518 2.213499 CTCACAAACTCAGGCTTTCGT 58.787 47.619 0.00 0.00 0.00 3.85
519 522 2.222027 CAAACTCAGGCTTTCGTCCTT 58.778 47.619 0.00 0.00 0.00 3.36
753 777 4.508128 CCCGTCCGTCCACGATGG 62.508 72.222 0.00 2.28 42.69 3.51
800 833 2.664851 CAGCGAGTGGACGGCAAA 60.665 61.111 0.00 0.00 0.00 3.68
812 845 0.827507 ACGGCAAATCCTTTGTGGCT 60.828 50.000 1.97 0.00 42.56 4.75
1012 1058 4.024670 AGACACTACTATGAACAGACCCC 58.975 47.826 0.00 0.00 0.00 4.95
1032 1078 2.484594 CCAAACCACCCCAAACATTGTC 60.485 50.000 0.00 0.00 0.00 3.18
1331 1384 6.756542 AGCAACCAAGAGTTAATTGAACAAAC 59.243 34.615 0.00 0.00 40.86 2.93
2195 3891 4.568152 ACAACAGTTATTTGAGTGCACC 57.432 40.909 14.63 5.76 0.00 5.01
2380 4083 6.039829 GGACTTTTCAGAACTTGTCCATCTTT 59.960 38.462 17.27 0.00 42.32 2.52
2503 4218 2.195922 GCAGCTTTGGTTCAACAAGTG 58.804 47.619 0.00 0.00 0.00 3.16
2559 4274 3.617263 GTGTGCCGGAACATAGTCTTAAG 59.383 47.826 20.89 0.00 31.49 1.85
2767 4482 6.524101 AACTGATACACAAAAACCACTTGT 57.476 33.333 0.00 0.00 37.49 3.16
2771 4487 7.106439 TGATACACAAAAACCACTTGTCAAT 57.894 32.000 0.00 0.00 34.80 2.57
2926 5150 1.299976 GGTTGGGCAGGTACCTCTG 59.700 63.158 12.84 3.78 37.79 3.35
3177 5413 2.104111 TGTCCTGAACTCGTGGAATTGT 59.896 45.455 0.00 0.00 0.00 2.71
3351 5590 3.314635 GCAAGCAGGATCAGTATTTGAGG 59.685 47.826 0.00 0.00 39.68 3.86
3775 6023 2.748605 GATGACGACACCATCATCTCC 58.251 52.381 6.92 0.00 45.20 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 116 2.094659 CGAAGTCCATCGCAACGCT 61.095 57.895 0.00 0.0 35.85 5.07
181 184 3.386237 GACTCCAGCAGGCCGTCT 61.386 66.667 0.00 0.0 34.33 4.18
400 403 1.217244 GTGGTAGGTGCCGTCGAAT 59.783 57.895 0.00 0.0 0.00 3.34
401 404 2.652530 GTGGTAGGTGCCGTCGAA 59.347 61.111 0.00 0.0 0.00 3.71
511 514 1.342555 CACGCGAACATAAGGACGAA 58.657 50.000 15.93 0.0 0.00 3.85
515 518 1.017177 GCACCACGCGAACATAAGGA 61.017 55.000 15.93 0.0 0.00 3.36
753 777 1.745087 ACGATTCCAACATGGCATCAC 59.255 47.619 0.00 0.0 39.66 3.06
798 831 1.428912 TCCAGGAGCCACAAAGGATTT 59.571 47.619 0.00 0.0 41.22 2.17
800 833 1.005215 CTTCCAGGAGCCACAAAGGAT 59.995 52.381 0.00 0.0 41.22 3.24
1012 1058 2.801342 CGACAATGTTTGGGGTGGTTTG 60.801 50.000 0.00 0.0 34.12 2.93
1032 1078 2.555199 CTCCCAAATAACTCAGGCTCG 58.445 52.381 0.00 0.0 0.00 5.03
1331 1384 6.092748 AGCAACAACCGCTTAGATTTTAATG 58.907 36.000 0.00 0.0 35.82 1.90
2195 3891 8.624776 AGTTCTGAACTTTCAATCTTTTACCTG 58.375 33.333 17.00 0.0 39.04 4.00
2380 4083 5.957771 ACTGATTTGATCCTTAGGTAGCA 57.042 39.130 0.00 0.0 0.00 3.49
2503 4218 6.593072 GCAATTTTACAAGGTTGCTCATTTC 58.407 36.000 0.00 0.0 42.61 2.17
2559 4274 2.985809 CTCGCATATGCTAGAGTGAAGC 59.014 50.000 24.56 0.0 36.09 3.86
2926 5150 9.411801 GGGAAAGAGATTCTAAATTTTCAACAC 57.588 33.333 0.00 0.0 38.18 3.32
3177 5413 3.585289 TGGCTAGTAGGGTGTGAAAATGA 59.415 43.478 0.00 0.0 0.00 2.57
3351 5590 5.575995 CGTAGTTCTTTGGGTAAACTAGCTC 59.424 44.000 0.00 0.0 36.46 4.09
3680 5925 2.631062 TCCCAACTTAGTGAGCTTCGAA 59.369 45.455 0.00 0.0 0.00 3.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.